Método de Wang-Landau para sequenciamento de aminoácidos em estrutura nativa de proteínas em modelos de rede

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Using genetic algorithm to design protein sequence

In this work, genetic algorithms concepts along with a rotamer library for proteins side chains are used to optimize the tertiary structure of the hydrophobic core of Cytochrome b(562) starting from the known PDB structure of its backbone which is kept fixed while the side chains of the hydrophobic core are allowed to adopt the conformations present in the rotamer library. The atoms of the side chains forming the core interact via van der Waals energy. Besides the prediction of the native core structure, it is also suggested a set of different amino acid sequences for this core. Comparison between these new cores and the native are made in terms of their volumes, van der Waals energies values and the numbers of contacts made by the side chains forming the cores. This paper proves that genetic algorithms area efficient to design new sequence for the protein core. (C) 2007 Elsevier B.V. All rights reserved.

Protein requirements for Blue-fronted Amazon (Amazona aestiva) growth

The objective of this study was to evaluate the protein requirements for hand-rearing Blue-fronted Amazon parrots (Amazona aestiva). Forty hatchlings were fed semi-purified diets containing one of four (as-fed basis) protein levels: 13%, 18%, 23% and 28%. The experiment was carried out in a randomized block design with the initial weight of the nestling as the blocking factor and 10 parrots per protein level. Regression analysis was used to determine relationships between protein level and biometric measurements. The data indicated that 13% crude protein supported nestling growth with 18% being the minimum tested level required for maximum development. The optimal protein concentration for maximum weight gain was 24.4% (p = 0.08; r(2) = 0.25), tail length 23.7% (p = 0.09; r(2) = 0.19), wing length 23.0% (p = 0.07; r(2) = 0.17), tarsus length 21.3% (p = 0.06; r(2) = 0.10) and tarsus width 21.4% (p = 0.07; r(2) = 0.09). Tarsus measurements were larger in males (p < 0.05), indicating that sex must be considered when studying developing psittacines. These results were obtained using a highly digestible protein and a diet with moderate metabolizable energy levels.

Protein levels and environmental temperature effects on carcass characteristics, performance, and nitrogen excretion of broiler chickens from 7 to 21 days of age

This trial was conducted to evaluate the utilization of low-protein diets formulated based on the ideal protein concept for broiler chickens from 7 to 21 days of age reared at different environmental temperatures. Nine hundred male Cobb-500® chickens were used. At day seven chicks were distributed according to a completely randomized design in a 3 x 3 factorial with four replications of 25 birds each. It was used three crude protein levels in the diet (21.5; 20.0 and 18.5%) and three environmental temperatures (low, thermoneutral and high). The performance, carcass characteristics (yield and chemical composition), and nitrogen ingestion and excretion were assessed. There was no significant interaction among the factors for the evaluated variables. Environmental temperatures affected differently chicken performance. High environmental temperature resulted in lower weight gain and higher wing fat percentage, whereas cold temperature resulted in higher feed conversion. on the other hand, low-protein diets decreased weight gain, breast yield, nitrogen excretion and influenced breast and wings chemical composition. Birds reared at high environmental temperature showed lower nitrogen intake and excretion. The results showed that the decrease in protein levels from 7 to 21 days of age contributed to lower nitrogen excretion in broiler chickens, but impaired performance and carcass characteristics independent of rearing temperature.

Effects of energy and protein levels on egg quality and performance of laying hens at early second production cycle

One hundred sixty-two commercial 70-wk-old ISA Brown laying hens, previously subjected to induced molting by feed restriction, were distributed in a completely randomized design with 3 x 3 factorial arrangement (i.e., 3 metabolizable energy levels: 2,850; 2,950, and 3,050 kcal of ME/kg) and 3 protein levels (16, 18, and 20% CP), which totaled 9 treatments with 3 replicates of 6 birds each. Experimental diets were offered to birds after the feed restriction period. Performance and egg quality parameters were evaluated in 14-d intervals from the 4th to 12th weeks after forced molting for a total of 4 evaluation periods. Increases in dietary energy and protein levels did not improve performance or egg quality. The levels of 2,850 kcal of ME and 16% protein were sufficient for laying hens starting the second production cycle without decreasing their performance or egg quality.

Effects of different sampling intervals on apparent protein and energy digestibility of common feed ingredients by juvenile oscar fish (Astronotus ocellatus)

O presente estudo avaliou a digestibilidade aparente da proteína e da energia de ingredientes (farelo de soja, farinha de peixe, farelo de trigo e milho) por juvenis de apaiari (Astronotus ocellatus) usando dois diferentes intervalos de coleta (30 min. e 12h). Os 160 juvenis de apaiari utilizados (22,37 ± 3,06 g de peso corporal) foram divididos em quatro tanques rede plásticos e cilíndricos, cada um colocado em um tanque de alimentação de 1.000 L. O experimento foi inteiramente casualizado em esquema fatorial 2 x 4 (2 intervalos de coleta de fezes e 4 ingredientes foram) com quatro repetições. Os testes estatísticos não detectaram efeito da interação entre o intervalo de coleta e tipo de ingrediente nos coeficientes de digestibilidade. O intervalo de coleta não afetou a digestibilidade da proteína e da energia. As características físicas das fezes dos juvenis de apaiari aparentemente as tornam menos sensíveis à perda de nutrientes por lixiviação, permitindo intervalos de coleta maiores. A digestibilidade da proteína dos ingredientes avaliados foi semelhante, mostrando que a digestibilidade aparente de ingredientes animais e vegetais por juvenis de apaiari é eficiente. Os coeficientes de digestibilidade da energia foram maiores para a farinha de peixe e o farelo de soja comparado a farelo de trigo e milho. Ingredientes ricos em carboidratos (farelo de trigo e milho) apresentaram os piores coeficientes de digestibilidade da energia e, portanto, não são usados eficientemente pelos juvenis de apaiari.

Small intestine development of laying hens fed different fiber sources diets and crude protein levels

The objective of the presente study was to evaluate the effects on different dietary fiber sources and crude protein levels on the intestinal morphometry of commercial layers. Isa Brown® layers with 48 weeks of age were distributed in a completely randomized experimental design with a 3 x 2 + 1 factorial arrangement, resulting in seven treatments with seven replicates of eight birds each. At the end of the fourth experimental period (28 days each), birds were 64 weeks of age and were randomly chosen (two birds per replicate, totaling 14 birds per treatment), weighed and sacrificed by neck dislocation. Their intestine was dissected and the duodenum, jejunum and ileum were collected for subsequent analysis of intestinal morphometry. Treatments consisted of diets containing three different fiber sources (cottonseed hulls, soybean hulls or rice husks) and two crude protein levels (12% or 16%). Soybean hulls and 16% crude protein level promoted, in general, an increase in villus height and crypt depth in the three intestinal segments. In the duodenum, the control diet resulted in higher villus height and crypt depth relative to the diets containing fiber. In the jejunum, higher crypt depth values. In the ileum, dietary fiber increased villus height as compared to the control diet.

Prediction equations to estimate the demand of energy and crude protein for maintenance, gain and egg production for laying Japanese quails

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Effects of different lipid levels on protozoa population, microbial protein synthesis and rumen degradability in cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Dried yeast (Saccharomyces cerevisae) as a protein source for horses

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Interleukin 18 messenger RNA and proIL-18 protein expression in chorioamniotic membranes from pregnant women with preterm prelabor rupture of membranes

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Plasmodium falciparum: sequence diversity and antibody recognition of the Merozoite surface protein-2 (MSP-2) in Brazilian Amazonia

The merozoite surface protein-2 (MSP-2) of Plasmodium falciparum comprises repeats flanked by dimorphic domains defining the allelic families FC27 and IC1. Here, we examined sequence diversity at the msp-2 locus in Brazil and its impact on MSP-2 antibody recognition by local patients. Only 25 unique partial sequences of msp-2 were found in 61 isolates examined. The finding of identical msp-2 sequences in unrelated parasites, collected 6-13 years apart, suggests that no major directional selection is exerted by variant-specific immunity in this malaria-endemic area. To examine antibody cross-reactivity, recombinant polypeptides derived from locally prevalent and foreign MSP-2 variants were used in ELISA. Foreign IC1-type variants, such as 3D7 (currently tested for human vaccination), were less frequently recognized than FC27-type and local IC1-type variants. Antibodies discriminated between local and foreign IC1-type variants, but cross-recognized structurally different local IC1-type variants. The use of evolutionary models of MSP-2 is suggested to design vaccines that minimize differences between local parasites and vaccine antigens. (C) 2004 Elsevier B.V. All rights reserved.

Molecular models of protein targets from Mycobacterium tuberculosis

Structural characterization of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design since some of these proteins may be present in the bacterial genome, but absent in humans. Thus, metabolic pathways became potential targets for drug design. The motivation of this work is the fact that Mycobacterium tuberculosis is the cause of the deaths of millions of people in the world, so that the structural characterization of protein targets to propose new drugs has become essential. DBMODELING is a relational database, created to highlight the importance of methods of molecular modeling applied to the Mycobacterium tuberculosis genome with the aim of proposing protein-ligand docking analysis. There are currently more than 300 models for proteins from Mycobacterium tuberculosis genome in the database. The database contains a detailed description of the reaction catalyzed by each enzyme and their atomic coordinates. Information about structures, a tool for animated gif image, a table with a specification of the metabolic pathway, modeled protein, inputs used in modeling, and analysis methods used in this project are available in the database for download. The search tool can be used for reseachers to find specific pathways or enzymes.

Immunolocalization of bone morphogenetic protein 2 during the early healing events after guided bone regeneration

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Design and synthesis of peptides from bacterial ParE toxin as inhibitors of topoisomerases

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)